flowcraft.templates.skesa module

Purpose

This module is intended execute Skesa on paired-end FastQ files.

Expected input

The following variables are expected whether using NextFlow or the main() executor.

• sample_id : Sample Identification string.

  • e.g.: 'SampleA'

• fastq_pair : Pair of FastQ file paths.

  • e.g.: 'SampleA_1.fastq.gz SampleA_2.fastq.gz'

• clear : If ‘true’, remove the input fastq files at the end of the

  component run, IF THE FILES ARE IN THE WORK DIRECTORY

Generated output

• ${sample_id}_*.assembly.fasta : Main output of skesawith the assembly

  • e.g.: sample_1_skesa.fasta

• clear : If ‘true’, remove the input fastq files at the end of the

  component run, IF THE FILES ARE IN THE WORK DIRECTORY

Code documentation

flowcraft.templates.skesa.clean_up(fastq)

Cleans the temporary fastq files. If they are symlinks, the link source is removed

Parameters:

fastq : list

List of fastq files.